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Protein sequence modules.

E Aharonovsky¹, E N Trifonov

¹Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel.

Journal of Biomolecular Structure & Dynamics

|October 13, 2005

Summary

This study introduces a new method to map protein conservation. It reveals that proteins are composed of conserved sequence modules, aiding in the identification of functional sites.

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Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

Conserved protein sequence segments are widely recognized as indicators of functional sites.
Existing methods often treat conservation as a uniform property across protein sequences.

Purpose of the Study:

To develop a novel approach for profiling the dynamic degree of protein sequence conservation.
To identify and characterize conserved sequence modules within proteins.

Main Methods:

Evaluating the occurrence frequencies of short oligopeptides within a given protein sequence against a large proteome database.
Generating protein sequence conservation profiles by analyzing oligopeptide frequencies.
Analyzing the resulting profiles to identify peaks representing conserved modules.

Main Results:

A method to plot protein sequence conservation profiles, highlighting potential functional sites.
Identified conserved oligopeptides are frequently found across numerous prokaryotic species.
All examined proteins exhibit a common feature: they comprise sequence modules marked by conservation peaks.
The typical distance between these conservation peaks (module size) is 25-30 amino acid residues.

Conclusions:

The proposed method effectively profiles sequence conservation, pinpointing functional regions.
Proteins are structured as modules of conserved sequences, offering insights into protein architecture.
This approach aids in the discovery and understanding of functionally important protein regions.

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